Expression markers of block hypomethylation

Gene sets defined using TCGA COAD

1. Genes upregulated with hypomethylation: coad_hypometh_up_genes.txt

2. Genes downregulated with hypomethylation: input/2020_johnstone_reyes_table_s5.txt

   This gene set is taken from Johnstone & Reyes 2020 and contains genes that are downregulated with hypomethylation, and includes additional filtering for non-immune infiltrate genes.

3. Gene expression ratio of the A vs B compartments

   This can be calculated as the expression ratio of coad_a_genes.txt and coad_b_genes.txt